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- PDB-4ah3: Crystal structure of the holo omega-transaminase from Chromobacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ah3 | ||||||
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Title | Crystal structure of the holo omega-transaminase from Chromobacterium violaceum | ||||||
![]() | OMEGA-TRANSAMINASE | ||||||
![]() | TRANSFERASE / AMINOTRANSFERASE | ||||||
Function / homology | ![]() adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sayer, C. / Isupov, M.N. / Littlechild, J.A. | ||||||
![]() | ![]() Title: Structural Studies with Pseudomonas and Chromobacterium [Omega]-Aminotransferases Provide Insights Into Their Differing Substrate Specificity. Authors: Sayer, C. / Isupov, M.N. / Westlake, A. / Littlechild, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 410.2 KB | Display | ![]() |
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PDB format | ![]() | 336.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 482.4 KB | Display | ![]() |
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Full document | ![]() | 520.8 KB | Display | |
Data in XML | ![]() | 88 KB | Display | |
Data in CIF | ![]() | 132.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b98C ![]() 4b9bC ![]() 4ba4C ![]() 4ba5C ![]() 1qj3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51279.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase #2: Chemical | ChemComp-PLP / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.6 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.22 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→26.73 Å / Num. obs: 218828 / % possible obs: 94.4 % / Observed criterion σ(I): 1.9 / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.57→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.9 / % possible all: 90.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QJ3 Resolution: 1.57→115.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.353 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.292 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→115.19 Å
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Refine LS restraints |
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